Biology: Definition and Cell Theory

Biology: Definition and Origins

• Biology is the scientific study of living organisms (plants, animals, and humans).
• The term originates from the Greek words "bio" (life) and "logy" (study).

Cell Theory

• All living organisms are composed of cells.
• Cells are the basic units of structure and function in organisms.
• New cells arise only from pre-existing cells.
• Key contributors include Schleiden, Schwann, and Virchow (19th century).
• Antoine van Leeuwenhoek first observed microorganisms.
• Robert Hooke coined the term "cell" in 1665.

Understanding Organisms

• Unicellular organisms consist of a single cell (e.g., bacteria).
• Multicellular organisms are composed of many cells (e.g., humans, plants).
• "Organum" is the Latin term for organism, highlighting its structure.

Cell Structure and Types

• All cells contain plasma membrane, DNA, and ribosomes.
• DNA and RNA are essential for protein synthesis and cell function.

Prokaryotic Cells

• Simple cells lacking a nucleus and membrane-bound organelles.
• Shapes include spherical, rod-like, and spiral.
• DNA is a single circular molecule.
• Cell walls and flagella/pili aid movement and attachment.

Eukaryotic Cells

• Complex cells with a nucleus and membrane-bound organelles.
• More specialized for complex tasks.
• Eukaryotic cells have a lower surface area-to-volume ratio than prokaryotic cells.

Eukaryotic Cell Structures and Functions

• Cytoplasm: Contains organelles for energy, synthesis, storage, and transport.
• Ribosomes: Free or attached, involved in protein synthesis.
• Endomembrane System: Includes nuclear envelope, ER, Golgi, lysosomes, and plasma membrane for protein synthesis and transport.
• Mitochondria: Perform cellular respiration, producing ATP.
• Cytoskeleton: Provides structural support, movement, and cell organization.

Plant vs. Animal Cells

• Animal cells: Contain lysosomes, centrioles, and flagella.
• Plant cells: Contain chloroplasts, central vacuole, tonoplast, and a cell wall, reflecting their different functions.

The Nucleus in Eukaryotic Cells

• Functions: Contains most of the cell's DNA.
• Structure:
  • Surrounded by a nuclear envelope with pores regulating molecule passage.
  • Nucleolus assembles ribosomes.
  • Chromatin forms chromosomes.

Microscopy Techniques

• Light microscopes use light for viewing specimens (e.g., bright-field, differential interference contrast, fluorescence).
• Electron microscopes use electrons for higher resolution images (e.g., transmission and scanning electron microscopy).
• Measurement units: µm (micrometers), nm (nanometers), and Å (angstroms).

Common Cell Elements

• Plasma membrane: Surrounds the cell, regulates substance flow (phospholipid bilayer).
• Cytoplasm: Contains organelles, site of metabolic processes.
• Chromosomes: Contain genetic material.
• Cytoskeleton: Provides structural integrity, facilitates cell movement.

Ribosomes

• Composition: Ribosomal RNA (rRNA) and proteins make up ribosomes.
• Function: Protein synthesis, located in cytosol or attached to the endoplasmic reticulum.
• Subunits: Large and small subunits work together in protein synthesis.

Endomembrane System

• Components: Nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane.
• Function: Coordinates protein synthesis, modification, and transport.

Endoplasmic Reticulum (ER)

• Smooth ER: Synthesizes lipids, regulates carbohydrate metabolism.
• Rough ER: Modifies and folds proteins, contains ribosomes.

Golgi Apparatus

• Structure: Flattened membranous sacs (cisternae).
• Function: Modifies ER products, synthesizes macromolecules; sorts and packages proteins.

Mitochondria and Chloroplasts

• Mitochondria: Perform cellular respiration, ATP production.
• Chloroplasts: Found in plant cells, conduct photosynthesis, produce food.

Peroxisomes

• Function: Involved in lipid metabolism, detoxification.

Cytoskeleton and Cellular Movements

• Cytoskeleton: Network of fibers organizing cell structures and activities.
  • Microtubules: Cell division, movement.
  • Centrosomes and Centrioles: Organize microtubules, cell division.
  • Microfilaments (actin): Muscle movements, cell division, cytoplasmic streaming.

Extracellular Components and Connections

• Extracellular structures: Cells produce materials outside the plasma membrane.
  • Plant cell walls: Provide structural support.
  • Animal extracellular matrix (ECM): Structural, biochemical support to cells.
  • Intercellular junctions: Facilitate cell communication, physical contact. (Tight junctions, gap junctions, desmosomes in animal; plasmodesmata in plants)

Intercellular Junctions

• Plant plasmodesmata: Membrane-lined pores enabling communication and transport of small molecules.
• Animal cell junctions:
  • Tight junctions: Prevent fluid leakage.
  • Desmosomes: Anchor cells, maintain structure.
  • Gap junctions: Provide channels for cell communication.

Fluid Mosaic Model

• Plasma membrane: Separates cells from surroundings, selectively permeable.
  • Structure: Phospholipid bilayer, embedded proteins.
    • Phospholipids: Hydrophilic heads, hydrophobic tails (bilayer).
    • Membrane proteins: Integral (spanning membrane), peripheral (surface attached), involved in transport, enzymatic activity, signal transduction, and cell recognition.
    • Membrane fluidity: Cholesterol maintains stability, varies with temperature.

Transport Mechanisms

• Passive transport: Movement with a concentration gradient without energy. (Diffusion, facilitated diffusion, osmosis)
• Active transport: Movement against concentration gradient requiring energy. (Primary, secondary active transport, e.g., sodium-potassium pump)
• Bulk transport: Movement of large materials. (Exocytosis, endocytosis)

Definitions of Cellular Structures

• Cell: Smallest functional unit of life.
• Nucleic acids: Carry genetic information (DNA/RNA).
• Cell membrane: Regulates cell's internal environment.
• Cell wall: Protection, support (plant cells).
• Gene: Segment of DNA, blueprint for traits.

Cellular Functions and Organelles

• Organelles: Specialized structures performing functions (ATP production, protein synthesis, cell structure).

Meiosis: Overview and Importance

• Meiosis: Cell division in sexually reproducing organisms, reducing chromosome number to form gametes (sperm/eggs).
• Significance: Ensures genetic diversity and stable chromosome number across generations.

Stages of Meiosis

• Meiosis I: Separates homologous chromosomes into two haploid cells.
• Meiosis II: Separates sister chromatids into four haploid cells. Key phases for both are included.

Key Terminology in Meiosis

• Gametes (sperm/eggs): Haploid reproductive cells.
• Zygote: Fertilized egg; restores diploid number.
• Bivalent: Homologous chromosome pair.
• Tetrad: Four chromatids during Prophase I.
• Crossing Over: Genetic material exchange during Prophase I.
• Haploid: Half the normal chromosome number.

Mechanisms of Genetic Variation

• Genetic variation primarily arises from crossing over and independent assortment in meiosis.
  • Crossing Over during Prophase I: Creates new allele combinations.
  • Independent Assortment during Metaphase I: Maternal/paternal chromosome combinations vary.

Significance of Genetic Variation

• Natural selection enables populations to adapt to changing environments.
• Used in agriculture for resilient crop breeding.
• Important for personalized medicine, understanding hereditary diseases.
• Crucial for conservation efforts.

Definition and Importance of Meiosis

• Meiosis: Specialized cell division reducing chromosome number, creating four distinct haploid cells (gametes). Essential for sexual reproduction, increasing diversity.

Stages of Meiosis

• Meiosis I: Homologous chromosomes separated, resulting in two haploid cells.
• Meiosis II: Similar to mitosis (separates sister chromatids), creating four haploid cells.

Major Events and Their Significance:

• Crossing-over, chiasmata, synapsis, independent assortment are detailed.

Comparison of Meiosis and Mitosis

• Mitosis produces two identical diploid cells.
• Meiosis produces four unique haploid cells.

Overview of the Cell Cycle

• Cell cycle: Series of events leading to cell division (growth, DNA replication, chromosome distribution).
• Phases: G1, S, G2, M (mitosis).
• Regulation: Checkpoints preventing errors. Cancer results from cycle disruptions.

Phases of the Eukaryotic Cell Cycle

• G1: Growth, preparing for DNA replication.
• S: DNA replication (doubling genetic material).
• G2: Further growth, organelle duplication.
• M: Mitosis and cytokinesis.

Comparison of Prokaryotic and Eukaryotic Cell Cycles

• Prokaryotes use binary fission (simpler).
• Eukaryotes have a complex cycle with specific phases.
• Prokaryotic chromosomes are circular; eukaryotic are linear.

Key Structures in Cell Division

• Spindle apparatus
• Centrosome
• Kinetochore
• Cleavage furrow (animal cells)
• Cell plate (plant cells)

Stages of Mitosis, in detail

• Prophase
• Prometaphase
• Metaphase
• Anaphase
• Telophase

Key Characteristics of Living Organisms

• Order
• Sensitivity
• Reproduction
• Growth and Development
• Regulation
• Homeostasis

Characteristics of Viruses

• Not true living organisms (lack metabolic processes, cannot independently reproduce).
• Structure: Protein coat surrounding DNA or RNA.
• Dependence on hosts.
• Controversy exists about their definition of life.

Theories on Life's Origins

• Oparin-Haldane Theory
• Miller-Urey Experiment
• Hypotheses on early environments (reducing atmosphere, deep-sea vents, extraterrestrial origins)

Significance of Oxygenic Photosynthesis

• Originated with cyanobacteria.
• Changed Earth's atmosphere by producing oxygen.
• Enabled aerobic respiration, more complex life.

The Rise of Oxygen

• Facilitated aerobic respiration, enabled complex life.
• Reshaped ecosystems, ozone layer.

Origin of Mitochondria and Chloroplasts

• Endosymbiotic theory (engulfed prokaryotic cells).
• Evidence (double membranes, circular DNA).
• Evolutionary significance in eukaryotic cell complexity.

Energy

• Capacity to do work, various forms (kinetic, potential, chemical, thermal).

The Laws of Thermodynamics

• First Law: Energy conservation.
• Second Law: Entropy increases.

Cellular Metabolism

• Overview: Catabolic, anabolic reactions.
• Energy balance maintains homeostasis.

Gibbs Free Energy

• Quantifies work potential in systems.
• Exergonic and endergonic reactions.

Role of Enzymes

• Lower activation energy to speed up reactions.
• Specificity to substrates.
• Factors influence activity (pH, temperature).

Enzyme Cofactors and Coenzymes

• Cofactors: Inorganic ions.
• Coenzymes: Organic molecules assisting enzymes.
• Prosthetic groups: Permanently attached cofactors.

ATP as an Energy Currency

• ATP: Primary energy carrier.
• Hydrolysis: Releases energy (ATP→ADP).

Mechanisms of ATP Generation

• Substrate-level phosphorylation
• Chemiosmosis (electron transport)

Overview of Bioenergy Carriers

• ATP: Main carrier.
• Electron transport linked to ATP synthesis.

Types of Phosphorylation

• Oxidative Phosphorylation (mitochondria)
• Photophosphorylation (chloroplasts)

Redox Reactions in Energy Transfer

• Definition (oxidation/reduction, electron transfer).
• Example (methane combustion).
• Importance in ATP production (glycolysis, citric acid cycle).

Key Electron Carriers

• NAD⁺, NADH, NADP⁺, FAD, FADH₂, cytochromes.
• Function: Facilitating electron transfer in metabolic pathways.

Energy of Activation

• Minimum energy needed for a chemical reaction.
• Enzymes lower activation energy.

Role of Enzymes in Metabolism

• Catalysts accelerating reactions.
• Specificity to substrates.
• Regulation through feedback and allosteric methods.

DNA Replication Overview

• Process: Copying DNA to produce two identical molecules.
  • Semiconservative Replication: One parental strand, one new strand in each new molecule. (Meselson-Stahl experiment).

Semi-conservative Replication Process

• Untwisting the helix (hydrogen bonds broken).
• Strand Separation.
• DNA polymerase adds nucleotides.
• Lagging strand: Okazaki fragments, joined by DNA ligase.

Key Enzymes and Proteins

• DNA helicase
• DNA polymerase
• Topoisomerase
• DNA ligase
• Single-stranded binding proteins
• DNA primase
• DNA clamp

Replication Origin

• Bacteria (single origin).
• Eukaryotes (multiple origins).

Gene Expression

• Process: DNA → RNA → Protein (central dogma).
• One Gene-One Enzyme Hypothesis (Beadle & Tatum): Each gene controls a specific enzyme.

Transcription

• Copying DNA into RNA (mRNA for proteins, ncRNA).
• Prokaryotes: Transcription & translation in cytoplasm.
• Eukaryotes: Transcription in nucleus, translation in cytoplasm.
• Gene components: Promoter, regulatory sequences, transcribed region, terminator.

The Genetic Code

• Codons (3-nucleotide sequences) specify amino acids.
• Start codon (AUG), stop codons (UAA, UGA, UAG). Redundant but not ambiguous. Universal.

Translation

• mRNA decoded by ribosomes to form a polypeptide (protein).
• Ribosome sites: A, P, E.
• tRNA carries amino acids, anticodon pairs with mRNA codons.
• Aminoacylation: Attaching amino acids to tRNA.

Gene Mutations

• Permanent DNA sequence changes.
  • Base substitutions (missense, silent, nonsense).
  • Frameshift mutations (insertions/deletions).

Ribosome Structure and Function

• Ribosomes (30S/50S): tRNA-binding sites (A, P, E). rRNA, not protein, catalyzes peptide bond formation.

Translation (Protein Synthesis)

• Initiation: mRNA binding, formation of initiation complex
• Elongation: Codon reading, peptide bond formation
• Termination: Stop codon recognition, release of polypeptide chain

Bioenergetics

• Photosynthesis (chloroplasts)
• Cellular Respiration (mitochondria)

Mitochondrion Function

• Location of aerobic respiration and ATP production.
• Double membrane, cristae (inner membrane folds).

Stages of Cellular Respiration

• Glycolysis (breakdown of glucose)

Chloroplast Structure

• Stroma (fluid)
• Thylakoid membranes
• Granum (stacks of thylakoids)

Light Energy and Photosynthesis

• Light composition
• Wavelengths absorbed by plant pigments

Photosynthetic Pigments

• Chlorophyll (a, b)
• Carotenoids

Photosystems

• Light-harvesting complex (antenna complexes)
• P700 (Photosystem I)
• P680 (Photosystem II)

Electron Transport

• Water splitting, oxygen release.
• Electron chain from PSII to PSI.
• Proton gradient generation.

Chemiosmosis (Photophosphorylation)

• ATP synthesis powered by proton gradient.

Noncyclic and Cyclic Electron Flow

• Noncyclic: ATP & NADPH production.
• Cyclic: More ATP production.

ATP and NADPH Production

• Chemical energy from converting light energy.
• Used in the Calvin Cycle

Carbon Fixation (Calvin Cycle)

• Stroma location
• CO₂ fixation by Rubisco
• G3P generation, sugar production

Products of Photosynthesis

• ATP, NADPH, & Oxygen.
• G3P: Starch, amino acids, fatty acids, sucrose.
• Light-Dependent reactions (light reactions), Light Independent reactions (Calvin Cycle)

Final Electron Acceptors

• Photophosphorylation: NADP⁺
• Oxidative Phosphorylation: Oxygen

Noncyclic Electron Flow

Cyclic Electron Flow

Comparison of photophosphorylation and oxidative phosphorylation

Explore the foundational concepts of biology, including the definition and origins of the field. Understand the cell theory and the significance of cells as the basic units of life. Learn about the contributions of key scientists and the difference between unicellular and multicellular organisms.